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d2597738cb4001f9385eac6a22cf4fa53bb8bfde
Commit Graph
1572 Commits
Author SHA1 Message Date
mvdbeek d2597738cb Make to_cwl compatible with pulsar 2025-05-12 10:54:56 +02:00
mvdbeek eb38fd8ec9 Merge branch 'release_24.2' into dev 2025-05-12 09:05:28 +02:00
John Chilton 219796f049 Implement paired_or_unpaired collections, list wizards. 2025-05-09 17:39:38 -04:00
John Chilton 518fa136d9 [WIP] Implement records - heterogenous dataset collections. 
Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
 2025-05-09 16:38:19 -04:00
Ahmed Hamid Awan d7fa1d19ce Merge pull request #19054 from jmchilton/tool_markdown 
Implement tool markdown reports.
 2025-05-06 20:49:30 +05:00
Marius van den Beek 79638b883a Merge pull request #19753 from bernt-matthias/env-fix-24.1 
Fix setting env and tags on resubmission
 2025-05-06 17:23:45 +02:00
mvdbeek b99112c337 Fix DataCollectionParameterModel factory 2025-05-06 14:23:23 +02:00
Marius van den Beek 507719beb5 Merge pull request #20162 from mvdbeek/yaml_parser_fixes_part2 
Yaml parser fixes part2
 2025-05-06 09:13:11 +02:00
John Chilton 4e4017c1be Merge pull request #20152 from jmchilton/collection_cleanup_2 
Fix certain cases of collection parameter handling during workflow execution.
 2025-05-05 15:45:36 -04:00
mvdbeek 7ed247059a Fix conditional parsing 2025-05-05 20:37:17 +02:00
mvdbeek fa3c19c2a4 Merge branch 'release_24.2' into dev 2025-05-05 16:52:31 +02:00
mvdbeek a53b4125aa Skip `param_value` filter if ref value is runtime value 
Fixes https://github.com/galaxyproject/galaxy/issues/20136
 2025-05-04 16:48:33 +02:00
John Chilton 9b0fb38a76 More workflow mapping test cases. 2025-05-03 10:21:17 -04:00
John Chilton f9e1022360 Test case for bug where workflow collection mapping interprets collection at wrong rank. 2025-05-03 10:21:17 -04:00
John Chilton 1f95f421c9 Tool markdown reports. 2025-05-02 11:25:21 -04:00
Marius van den Beek 01e36311a4 Merge pull request #19954 from bernt-matthias/ext-lower 
Use lower case extension for setting datatype in data discovery
 2025-04-16 12:52:23 +02:00
mvdbeek 29d3c23cf2 Merge branch 'release_24.2' into dev 2025-04-15 17:53:08 +02:00
Marius van den Beek a8cf438ec5 Merge pull request #19763 from jmchilton/missing_functional_tool 
Add missing test file.
 2025-04-15 15:09:42 +02:00
Marius van den BeekandM Bernt e2647616c5 Fix typo 
Co-authored-by: M Bernt <m.bernt@ufz.de>
 2025-04-15 15:09:32 +02:00
Marius van den Beek 7a1ea09e9c Merge pull request #19949 from jmchilton/parameter_model_fixes_0 
[24.2] Fix various parameter validation issues.
 2025-04-15 15:08:28 +02:00
mvdbeek 6edab86870 Merge branch 'release_24.2' into dev 2025-04-10 18:54:17 +02:00
mvdbeek 4f9180604f Make dbkey_filter_input more realistic, regression test for https://github.com/galaxyproject/galaxy/issues/19975 2025-04-10 16:59:09 +02:00
Matthias Bernt e612db1680 extend tests 2025-04-03 10:32:50 +02:00
John Chilton f37075c1a5 Fix various parameter validation issues. 
I previously failed to include a bunch of validation checks I assumed had been covered so fixed that first and got a bunch of new issues detected. Also added a parameter specification test case for https://github.com/galaxyproject/galaxy/issues/19908 and fixed that.
 2025-04-02 12:49:09 -04:00
Matthias Bernt 0c186b227e fix test 2025-03-26 18:07:57 +01:00
Matthias Bernt ef72ecbb66 remove tool test assertions 2025-03-26 17:37:17 +01:00
Matthias Bernt 5b017b240f fix test 
tool fails with no env var set
failing tool tests allow no output
 2025-03-26 13:52:29 +01:00
Matthias Bernt 0247be1866 fix test tool test 2025-03-26 13:52:22 +01:00
Matthias Bernt 70bfcc44dc fix resubmission integration test 
the test `test/integration/test_job_resubmission.py::TestJobResubmissionToolDetectedErrorResubmitsIntegration`
resubmits with:

```
        <destination id="local_resubmit" runner="local">
            <env id="GX_TARGET_EXIT_CODE">4</env>
            <resubmit condition="tool_detected_failure" destination="local_good" />
        </destination>

        <destination id="local_good" runner="local">
            <env id="GX_TARGET_EXIT_CODE">0</env>
        </destination>
```

since env variables are lost on resubmission the current test
was still evaluated successful (because `${GX_TARGET_EXIT_CODE:-0}`).
Now the test fails if `GX_TARGET_EXIT_CODE` is not set.
 2025-03-26 13:52:08 +01:00
mvdbeek 3c6b6c5971 Merge branch 'release_24.2' into dev 2025-03-26 09:51:08 +01:00
mvdbeek 3c12acb270 Assert column_types 2025-03-25 10:29:01 +01:00
mvdbeek 8622dfa237 Merge branch 'release_24.2' into dev 2025-03-14 09:32:27 +01:00
mvdbeek 858593a8ba Fix transfer of $_TOOL_DIRECTORY subdirectories 
Goes together with https://github.com/galaxyproject/pulsar/pull/385
 2025-03-13 16:19:10 +01:00
mvdbeek eb1709fcbb Merge branch 'release_24.2' into dev 2025-03-08 11:20:03 +01:00
Marius van den Beek 54de00e2cf Merge pull request #19694 from mvdbeek/bwa_index_directory_datatype 
[24.2] Add bwa_mem2_index directory datatype, framework enhancements for testing directories
 2025-03-08 11:14:52 +01:00
John Chilton cc14cb4719 Missing test file. 2025-03-07 10:14:50 -05:00
mvdbeek ab2f7c3b57 Merge branch 'release_24.2' into dev 2025-02-28 12:34:02 +01:00
Marius van den BeekandBjörn Grüning e6b27a32b2 Adjust test tool and datatype config to best practices 
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
 2025-02-26 13:18:25 +01:00
mvdbeek 07a4a7c058 Fix directory uploads, use `__FETCH_DATA__` api 
for tool tests, which were still using upload1.
 2025-02-25 18:10:10 +01:00
John Chilton 387ce7dd37 Add failing test case for #19678 2025-02-25 11:39:58 -05:00
mvdbeek 6512b4c366 Add bwa_mem2_index datatype 2025-02-19 17:26:09 +01:00
John Davis 5cf48dc995 Merge remote-tracking branch 'upstream/release_24.2' into dev 2025-02-14 17:05:07 -05:00
mvdbeek 871a6901be Test sanitization 2025-02-11 14:36:20 +01:00
mvdbeek 2e6841680c Merge branch 'release_24.1' into release_24.2 2025-01-28 15:55:05 +01:00
mvdbeek 6006816033 Add regression test for https://github.com/galaxyproject/galaxy/issues/19245 2025-01-27 15:35:42 +01:00
mvdbeek f65b754dd0 Add regression test for https://github.com/galaxyproject/galaxy/issues/19245 2025-01-10 18:55:08 +02:00
mvdbeek b88a792b93 Merge branch 'release_24.2' into dev 2024-12-20 11:19:56 +01:00
mvdbeek 962839d68d Merge branch 'release_24.1' into release_24.2 2024-12-20 11:19:12 +01:00
Marius van den BeekandNicola Soranzo d66555ec1e ... 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-12-19 16:54:03 +01:00
Marius van den Beek 5c2a471afa Fix branch reference 2024-12-19 15:47:09 +01:00